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   &#160;<span id="projectnumber">0.4.3</span>
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      <li><a href="#index_m"><span>m</span></a></li>
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      <li><a href="#index_q"><span>q</span></a></li>
      <li><a href="#index_r"><span>r</span></a></li>
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      <li><a href="#index_t"><span>t</span></a></li>
      <li><a href="#index_v"><span>v</span></a></li>
      <li><a href="#index_x"><span>x</span></a></li>
      <li><a href="#index_y"><span>y</span></a></li>
      <li><a href="#index_z"><span>z</span></a></li>
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&#160;

<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
<li>atoms
: <a class="el" href="classmoltk_1_1PDBStructure.html#aa339055bdae2959af8baa08363630be5">moltk::PDBStructure</a>
</li>
</ul>


<h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
<li>b_end_gaps_free
: <a class="el" href="classmoltk_1_1MatrixScorer__.html#a69dc9913654f395b8a6912cd5866edc7">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
<li>chains
: <a class="el" href="classmoltk_1_1PDBStructure.html#a1bcb7d83816e73d4bc21fbb46ce27220">moltk::PDBStructure</a>
</li>
<li>character_indices
: <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a1f1a2d056adae546b8c191c37da99059">moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
<li>default_gap_extension_score
: <a class="el" href="classmoltk_1_1MatrixScorer__.html#ae46f2161ce2413aa901cfe80d79b4ac3">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>default_gap_open_score
: <a class="el" href="classmoltk_1_1MatrixScorer__.html#aa6e2fb51837602663ca39a4ba1b9fa3f">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>description
: <a class="el" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">moltk::Biosequence</a>
</li>
</ul>


<h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
<li>e
: <a class="el" href="structmoltk_1_1dp_1_1DPCell.html#af62bf28ecf418b8270fe93086e1c77e6">moltk::dp::DPCell&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>e_string
: <a class="el" href="classmoltk_1_1Alignment___1_1Row.html#a9d30e8fb78dcfa20b626c9055e3e6c49">moltk::Alignment_&lt; SCORE_TYPE &gt;::Row</a>
</li>
<li>eString1
: <a class="el" href="structmoltk_1_1dp_1_1AlignmentResult.html#a6c76ec9b71ae8f8951779dc502e5d0c3">moltk::dp::AlignmentResult&lt; SCORE_TYPE &gt;</a>
</li>
<li>eString2
: <a class="el" href="structmoltk_1_1dp_1_1AlignmentResult.html#a161ff0842e4aab4856065e40b69c2b72">moltk::dp::AlignmentResult&lt; SCORE_TYPE &gt;</a>
</li>
<li>extension_penalties
: <a class="el" href="structmoltk_1_1dp_1_1GapScore.html#a070815af7e6eeedf2403262135cc4b1b">moltk::dp::GapScore&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>extension_score
: <a class="el" href="structmoltk_1_1dp_1_1GapScore_3_01SCORE__TYPE_00_011_01_4.html#ae2711119af3ca77c215731c5cca4fc85">moltk::dp::GapScore&lt; SCORE_TYPE, 1 &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
<li>f
: <a class="el" href="structmoltk_1_1dp_1_1DPCell.html#aaa778620770caf52a6551edea6ee6dfd">moltk::dp::DPCell&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
<li>g
: <a class="el" href="structmoltk_1_1dp_1_1DPCell.html#a046ff4044916a1c22506e9db6e6ee5d8">moltk::dp::DPCell&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>gap_score
: <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html#aa50261e7c331d85a5f1828824c0f2961">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html#a7e0e60ba283915c7455ed3ecbe3f3cf3">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
<li>index
: <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html#a9ec521cd2e480623015d70abe23fd97c">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html#a8406700a74a939ac9732fcbf6da83a1b">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_l"></a>- l -</h3><ul>
<li>list
: <a class="el" href="classmoltk_1_1Alignment___1_1Row.html#ab797eb0dfbf30a2db2e2f3673aee5bf6">moltk::Alignment_&lt; SCORE_TYPE &gt;::Row</a>
</li>
<li>list_index
: <a class="el" href="classmoltk_1_1Alignment___1_1Row.html#a40eec6b995d925971d17c072dbf03998">moltk::Alignment_&lt; SCORE_TYPE &gt;::Row</a>
</li>
</ul>


<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
<li>m_score
: <a class="el" href="classmoltk_1_1Alignment__.html#ac929115e5fbbfb6a16f537f0d024ff72">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
<li>m_total_length
: <a class="el" href="classmoltk_1_1EString.html#a2900d588fd81ac22258b3039dc367a62">moltk::EString</a>
</li>
<li>m_ungapped_length
: <a class="el" href="classmoltk_1_1EString.html#af930d7290e6b6a0be911a194069c2cfa">moltk::EString</a>
</li>
<li>m_v
: <a class="el" href="classmoltk_1_1Quaternion.html#ab998e6f84008e4abdfabe7aa3bd6938e">moltk::Quaternion</a>
</li>
<li>m_w
: <a class="el" href="classmoltk_1_1Quaternion.html#a07b24f7e09fc61291b039471d1f6796d">moltk::Quaternion</a>
</li>
<li>m_x
: <a class="el" href="classmoltk_1_1BaseVector3D.html#a39f0a00c5acc2bc422efdd432c85c582">moltk::BaseVector3D&lt; ELT &gt;</a>
</li>
<li>m_y
: <a class="el" href="classmoltk_1_1BaseVector3D.html#a01edefd8c1d387619e20c55bdf971487">moltk::BaseVector3D&lt; ELT &gt;</a>
</li>
<li>m_z
: <a class="el" href="classmoltk_1_1BaseVector3D.html#a54781744a46fc5e925a7820e5d9ec764">moltk::BaseVector3D&lt; ELT &gt;</a>
</li>
<li>matrix
: <a class="el" href="classmoltk_1_1MatrixScorer__.html#a4bf1242ff86ad47455d09ce4df1a18e7">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
, <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a414f1e260f700d726aa9970af5edbd5c">moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_o"></a>- o -</h3><ul>
<li>one_letter_code
: <a class="el" href="classmoltk_1_1BiosequenceResidue.html#aaf62de3105859d585605982f72e127e3">moltk::BiosequenceResidue</a>
, <a class="el" href="classmoltk_1_1PDBStructure_1_1Residue.html#a3c8100085d64fb0b54fc90358af3c327">moltk::PDBStructure::Residue</a>
</li>
<li>open_penalties
: <a class="el" href="structmoltk_1_1dp_1_1GapScore.html#a9feedc029525367aad2523a8d0faacae">moltk::dp::GapScore&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>open_score
: <a class="el" href="structmoltk_1_1dp_1_1GapScore_3_01SCORE__TYPE_00_011_01_4.html#ac24f575197ec7bf84af487774d6be35a">moltk::dp::GapScore&lt; SCORE_TYPE, 1 &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
<li>position_index
: <a class="el" href="classmoltk_1_1EString_1_1const__iterator.html#a9997888176246e21da82d252d96638a7">moltk::EString::const_iterator</a>
</li>
<li>pretty_width
: <a class="el" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_q"></a>- q -</h3><ul>
<li>query_positions
: <a class="el" href="structmoltk_1_1dp_1_1DPTable_3_01SCORE__TYPE_00_01DP__MEMORY__LARGE_00_01ALIGN__TYPE_00_011_01_4.html#aedce8c28f14fc59d5bcfda67e8e6c6ca">moltk::dp::DPTable&lt; SCORE_TYPE, DP_MEMORY_LARGE, ALIGN_TYPE, 1 &gt;</a>
</li>
<li>query_residue_type_index_weights
: <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html#a4c9bac0ed963c8c1e1f442453f2e2084">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html#a452c100474707a26a22c3cfcc66a7b60">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
<li>record_type
: <a class="el" href="classmoltk_1_1PDBStructure_1_1Atom.html#af755f6dac2b1915a257146662e3ae5e7">moltk::PDBStructure::Atom</a>
</li>
<li>residue_number
: <a class="el" href="classmoltk_1_1BiosequenceResidue.html#aadadea46d0a17dc35ff54f543e42f460">moltk::BiosequenceResidue</a>
, <a class="el" href="classmoltk_1_1PDBStructure_1_1Residue.html#af013d260c48c242417b7e4a16900be33">moltk::PDBStructure::Residue</a>
</li>
<li>residues
: <a class="el" href="classmoltk_1_1PDBStructure_1_1Chain.html#a759a8771e9442c21cf51fc1a140c3216">moltk::PDBStructure::Chain</a>
</li>
<li>rotation
: <a class="el" href="classmoltk_1_1RigidTransform.html#a42cf4e9489a15f72c675aa1e2cea82e2">moltk::RigidTransform</a>
</li>
<li>row0
: <a class="el" href="classmoltk_1_1Rotation3D.html#a400503bde84c8198dfd791f29b7be91c">moltk::Rotation3D</a>
</li>
<li>row1
: <a class="el" href="classmoltk_1_1Rotation3D.html#a69bdf57177ae3bdf6738020d115306a5">moltk::Rotation3D</a>
</li>
<li>row2
: <a class="el" href="classmoltk_1_1Rotation3D.html#a9cbd4ba1b41c2387dde1b17ca4145c32">moltk::Rotation3D</a>
</li>
<li>rows
: <a class="el" href="classmoltk_1_1Alignment__.html#a468e2e5c2a46fb3b163805942a533c08">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
<li>run_index
: <a class="el" href="classmoltk_1_1EString_1_1const__iterator.html#a4023b95df1ce183cabeea986e0f3e4a0">moltk::EString::const_iterator</a>
</li>
<li>runs
: <a class="el" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">moltk::EString</a>
, <a class="el" href="classmoltk_1_1EString_1_1const__iterator.html#a3491024e82a7e6604138b9821cd61cac">moltk::EString::const_iterator</a>
</li>
</ul>


<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
<li>score
: <a class="el" href="structmoltk_1_1dp_1_1RunningScore.html#a5814258bbf4fee728de4eb83486b32ed">moltk::dp::RunningScore&lt; SCORE_TYPE &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__UNGAPPED__SEQUENCES_00_011_01_4.html#a4f927e74dfc33e81d635b08e074d7582">moltk::dp::RunningGapScore&lt; SCORE_TYPE, DP_ALIGN_UNGAPPED_SEQUENCES, 1 &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1AlignmentResult.html#a8a554558c4efa955f56e4855be1e8136">moltk::dp::AlignmentResult&lt; SCORE_TYPE &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__GAPPED__ALIGNMENTS_00_011_01_4.html#a44d662dc9b3b6a78e987fae51442f20a">moltk::dp::RunningGapScore&lt; SCORE_TYPE, DP_ALIGN_GAPPED_ALIGNMENTS, 1 &gt;</a>
</li>
<li>scorer
: <a class="el" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">moltk::Aligner</a>
</li>
<li>sequence_index
: <a class="el" href="classmoltk_1_1EString_1_1const__iterator.html#aebfe683ee618731fb3548e2f6a6d16f4">moltk::EString::const_iterator</a>
</li>
<li>sequence_weight
: <a class="el" href="classmoltk_1_1Alignment___1_1Row.html#a655f1804f8dd752f58c3c8c9ba0349c0">moltk::Alignment_&lt; SCORE_TYPE &gt;::Row</a>
</li>
<li>sequences
: <a class="el" href="classmoltk_1_1Alignment__.html#afb22dd1d74614d10f0633ce8bfb2f6a6">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
<li>SIZE
: <a class="el" href="classmoltk_1_1BaseVector3D.html#a3624a981da731d31bae9b31cedebddb1">moltk::BaseVector3D&lt; ELT &gt;</a>
</li>
<li>structures
: <a class="el" href="classmoltk_1_1Alignment__.html#ab7ef21f5246cf6aeeb64e199d02ff8fa">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
<li>table
: <a class="el" href="structmoltk_1_1dp_1_1DPTable_3_01SCORE__TYPE_00_01DP__MEMORY__LARGE_00_01ALIGN__TYPE_00_011_01_4.html#a0aaff051f5c99bf16b58f4fc75b8bdc5">moltk::dp::DPTable&lt; SCORE_TYPE, DP_MEMORY_LARGE, ALIGN_TYPE, 1 &gt;</a>
</li>
<li>target_positions
: <a class="el" href="structmoltk_1_1dp_1_1DPTable_3_01SCORE__TYPE_00_01DP__MEMORY__LARGE_00_01ALIGN__TYPE_00_011_01_4.html#a1bc69b4945577e1a2c8a8fa30af096a0">moltk::dp::DPTable&lt; SCORE_TYPE, DP_MEMORY_LARGE, ALIGN_TYPE, 1 &gt;</a>
</li>
<li>target_scores_by_residue_type_index
: <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html#a7c1eb245d8e63ca00cfe4f06ad781a45">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html#ab18850c77a8b837392b3112722e317da">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt;</a>
</li>
<li>test_table
: <a class="el" href="classmoltk_1_1Aligner.html#a683da4069fec5bc5b2766792b8f37c04">moltk::Aligner</a>
</li>
<li>translation
: <a class="el" href="classmoltk_1_1RigidTransform.html#a8ac08cb8d6e8d767bb4125be47ad5cde">moltk::RigidTransform</a>
</li>
</ul>


<h3><a class="anchor" id="index_v"></a>- v -</h3><ul>
<li>v
: <a class="el" href="structmoltk_1_1dp_1_1DPCell.html#aa46b7ac2c0aebc170df9229b714cab63">moltk::dp::DPCell&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>value
: <a class="el" href="structmoltk_1_1units_1_1Quantity.html#afaf8597b93b604c3980218dceefff4c8">moltk::units::Quantity&lt; U, Y &gt;</a>
</li>
</ul>


<h3><a class="anchor" id="index_x"></a>- x -</h3><ul>
<li>x
: <a class="el" href="classmoltk_1_1Rotation3D_1_1Row.html#a1d83281fbbcbeba3851a533e77f892fb">moltk::Rotation3D::Row</a>
</li>
</ul>


<h3><a class="anchor" id="index_y"></a>- y -</h3><ul>
<li>y
: <a class="el" href="classmoltk_1_1Rotation3D_1_1Row.html#a2d7ea2a03848b77c0c785c85142a324e">moltk::Rotation3D::Row</a>
</li>
</ul>


<h3><a class="anchor" id="index_z"></a>- z -</h3><ul>
<li>z
: <a class="el" href="classmoltk_1_1Rotation3D_1_1Row.html#a427766856690a138552876a896ca0969">moltk::Rotation3D::Row</a>
</li>
</ul>
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